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Merged
drroe merged 41 commits into from
Jun 7, 2022
Merged

Extend GIST to mixtures and non-water solvents #961

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db80756
Update GIST description with new command line options.
fwaibl Feb 22, 2022
4aeb30d
in GIST, remove excludeions option
fwaibl Feb 22, 2022
fb2366b
In GIST, add a function to create datasets, change griddim_ to int.
fwaibl Feb 28, 2022
95b7294
in GIST, refactor creation of the O_idxs array etc.
fwaibl Feb 28, 2022
97e7ad6
Unfinished implementation of GIST with non-water solvents.
fwaibl Mar 3, 2022
2cf17cf
Make GIST datasets dynamic to allow other elements than O and H.
fwaibl Mar 7, 2022
d9a9f4e
Further GIST updates and refactorings
fwaibl Mar 8, 2022
61782bc
In GIST, redo some bad refactorings of the prior commits
fwaibl Mar 10, 2022
463c6fe
Fix GIST output
fwaibl Mar 10, 2022
1386881
In GIST, track molecular densities and set rigidatomindices
fwaibl Mar 17, 2022
f6a74dd
In GIST: Consistent energy between PME and CPU, update tests
fwaibl Mar 18, 2022
89d6499
Parallel entropy and RAM improvement for GIST.
fwaibl Mar 21, 2022
332fbec
In GIST, fix progress bar for entropy, use "nocom" in GIST tests.
fwaibl Mar 23, 2022
ad8aa7c
In GIST, fix timing of CUDA energy being double-counted
fwaibl Mar 23, 2022
018eae0
In GIST, rename N_waters_ to N_solvent_ and update tests.
fwaibl Apr 4, 2022
298f245
Undo an accidental change (extra echo command) in MasterTest.sh
fwaibl Apr 4, 2022
2c9f37f
Update a format string in GIST
fwaibl Apr 5, 2022
3fba0b3
Add .save files for GIST entropy tests
fwaibl Apr 5, 2022
fbf3672
Fix a segmentation fault in GIST.
fwaibl Apr 5, 2022
d11ec5b
Avoid the arccos call in GIST orientational entropy.
fwaibl Apr 27, 2022
01efa0c
Add a GIST test for the entropy of a multidimensional normal distribu…
fwaibl Apr 28, 2022
287f705
In GIST, increase test tolerance to 1.1E-4
fwaibl Apr 29, 2022
20e148b
Split GIST energy into solvent molecules, not yet correct!
fwaibl May 2, 2022
7ba9de8
Fix double counting in GistCudaCalc.cu
fwaibl May 3, 2022
eec435b
Add GIST tests for salt-water mixture
fwaibl May 5, 2022
6c7286c
Add regression tests for GIST energy with ions
fwaibl May 6, 2022
fa5ecf8
Check for libpme in GIST tests
fwaibl May 6, 2022
a2f42ef
Add test tolerance to the Test_GIST_Order tests
fwaibl May 6, 2022
f396794
Fix GIST test runner.
fwaibl May 6, 2022
ffce306
In GIST, streamline neighbor calculation with energy
fwaibl Jun 1, 2022
874b0f6
Minor GIST updates
fwaibl Jun 1, 2022
1143301
Update documentation for GIST
fwaibl Jun 1, 2022
499b974
Add references to GIST, add tolerance to new GIST test.
fwaibl Jun 2, 2022
a2f2ecd
Merge branch 'Amber-MD:master' into mixtures
fwaibl Jun 2, 2022
1ea134a
Merge branch 'mixtures' of github.com:fwaibl/cpptraj into mixtures
fwaibl Jun 2, 2022
3c906b0
Increase version number to 6.7.0
fwaibl Jun 2, 2022
37cbf98
Add .save files for GIST test with benzene as a solvent
fwaibl Jun 2, 2022
a74c4ff
Fix a print formatting string in GIST
fwaibl Jun 3, 2022
84561f1
Merge branch 'master' into mixtures
fwaibl Jun 3, 2022
93ee243
more exact quaternion distance in GIST
fwaibl Jun 7, 2022
d358625
Merge branch 'mixtures' of github.com:fwaibl/cpptraj into mixtures
fwaibl Jun 7, 2022
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272 changes: 237 additions & 35 deletions doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -25801,10 +25801,6 @@ rdval>]
[noimage] Disable distance imaging in energy calculation.
\end_layout

\begin_layout Description
[excludeions] If specified, exclude any ions from the calculation.
\end_layout

\begin_layout Description

\series bold
Expand Down Expand Up @@ -25988,6 +25984,68 @@ suffix>] Suffix for main GIST info file name.
the calculation time (default 1).
\end_layout

\begin_layout Description
[solute
\begin_inset space ~
\end_inset

<mask>] Selection mask for the solute.
All other molecules will be solvent.
If this is omitted, the standard solute/solvent assignment will be used.
\end_layout

\begin_layout Description
[solventmols
\begin_inset space ~
\end_inset

<MOLS>] Comma-separated list of names of solvent molecules.
Energies will be computed per solvent molecule.
For the entropy, only the main solvent (the first one) will be used.
Use, e.g.,
\series bold
solventmols WAT,NA,CL
\series default
for a GIST calculation including ions.
This needs to be specified if there is more than one solvent species.
\end_layout

\begin_layout Description
[nocom] Do not use the center of mass to define the molecular position.
Instead, use the first atom in
\series bold
rigidatoms
\series default
.
Use this flag to restore the behavior of old GIST runs.
\end_layout

\begin_layout Description
[rigidatoms
\begin_inset space ~
\end_inset

<CENTRAL>
\begin_inset space ~
\end_inset

<SUBST1>
\begin_inset space ~
\end_inset

<SUBST2>] Specifies how to define the molecular orientation for the entropy.
By default, a simple heuristic will be used.
This works for water, but not for all solvents.
The atoms should be representative of the molecular orientation and should
not be collinear.
Note that the central atom goes first.
For water, the default is equivalent to
\series bold
rigidatoms O H1 H2
\series default
, corresponding to H1-O-H2 as the rigid substructure.
\end_layout

\begin_layout Description
[nopme] Do not use particle mesh Ewald for the non-bonded calculation (default).
\end_layout
Expand Down Expand Up @@ -26105,7 +26163,11 @@ DataSet Aspects:
\end_layout

\begin_layout Description
[dTSorient] First order orientational entropy density .
[dTSorient] First order orientational entropy density.
\end_layout

\begin_layout Description
[dTSsix] First order six-dimensional entropy density.
\end_layout

\begin_layout Description
Expand Down Expand Up @@ -26145,6 +26207,90 @@ DataSet Aspects:
[U_PME] (pme only) Mean solute energy on the GIST grid.
\end_layout

\begin_layout Standard
DataSets if the main solvent is not water:
\end_layout

\begin_layout Description
[gELEM] For every element
\series bold
ELEM
\series default
in the main solvent, the atomic density relative to rho0 (e.g.,
\series bold
gC
\series default
and
\series bold
gH
\series default
for benzene).
\end_layout

\begin_layout Standard
DataSets if there are multiple solvents:
\end_layout

\begin_layout Description
[g_mol_NAME] for every solvent species
\series bold
NAME
\series default
(e.g.,
\series bold
g_mol_WAT
\series default
and
\series bold
g_mol_NA
\series default
if
\series bold
solventmols WAT,NA
\series default
was specified).
\end_layout

\begin_layout Description
[Esw_mol_NAME] for every solvent species
\series bold
NAME
\series default
(e.g.,
\series bold
Esw_mol_WAT
\series default
and
\series bold
Esw_mol_NA
\series default
if
\series bold
solventmols WAT,NA
\series default
was specified).
\end_layout

\begin_layout Description
[Eww_mol_NAME] for every solvent species
\series bold
NAME
\series default
(e.g.,
\series bold
Eww_mol_WAT
\series default
and
\series bold
Eww_mol_NA
\series default
if
\series bold
solventmols WAT,NA
\series default
was specified).
\end_layout

\end_deeper
\begin_layout Standard
Grid Inhomogeneous Solvation Theory
Expand Down Expand Up @@ -26519,6 +26665,37 @@ g_H

\begin_layout Itemize

\series bold
g_ELEM
\series default
- (if the main solvent is not water) Density of every further element
\series bold
ELEM
\series default
in the main solvent.
Scaled such that the expectation value in pure solvent is unity.
\end_layout

\begin_layout Itemize

\series bold
g_mol_NAME
\series default
- (if there is more than one solvent) Density of every solvent species

\series bold
NAME
\series default
specified in solventmols.
Scaled by
\series bold
rho0
\series default
.
\end_layout

\begin_layout Itemize

\series bold
dTStrans-dens
\series default
Expand Down Expand Up @@ -26625,8 +26802,60 @@ unting, and not referenced to the corresponding bulk value of this quantity
\end_inset

).
Again, both Lennard-Jones and electrostatic interactions are computed without
any cutoff, within the minimum image convention.
Unless PME is used, both Lennard-Jones and electrostatic interactions are
computed without any cutoff, within the minimum image convention.
\end_layout

\begin_layout Itemize

\series bold
Esw_mol_NAME-dens
\series default
and
\series bold
Esw_mol_NAME-norm
\series default
- (if there are multiple solvent species) Mean solute-solvent energy per
molecule of species
\series bold
NAME
\series default
, for each solvent specified in
\series bold
solventmols
\series default
.
Follows the same conventions as
\series bold
Esw
\series default
.
\end_layout

\begin_layout Itemize

\series bold
Eww_mol_NAME-dens
\series default
and
\series bold
Eww_mol_NAME-norm
\series default
- (if there are multiple solvent species) Mean solvent-solvent energy per
molecule of species
\series bold
NAME
\series default
, for each solvent specified in
\series bold
solventmols
\series default
.
Follows the same conventions as
\series bold
Eww
\series default
.
\end_layout

\begin_layout Itemize
Expand Down Expand Up @@ -27541,34 +27770,7 @@ d with a region
can add up quickly.
It can be advisable to omit all voxels above a certain distance to the
solute to obtain more stable results.
When using PME, the energy cannot be decomposed into Eww and Esw contributions.
In that case, the energy of hydration is
\begin_inset Formula $\Delta E_{hyd}=E_{solute}-E_{solute}^{self}+\sum^{voxels}E_{PME}^{dens}\times V_{vox}$
\end_inset

, where the solute energy
\begin_inset Formula $E_{solute}$
\end_inset

(containing solute-solute and solute-solvent interactions) can be found
in the GIST
\series bold
info
\series default
file, and the solute self-energy
\begin_inset Formula $E_{solute}^{self}$
\end_inset

can be obtained e.g.
using the
\begin_inset Quotes eld
\end_inset

energy
\begin_inset Quotes erd
\end_inset

command .

\end_layout

\begin_layout Subsection
Expand Down
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